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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. Software tools which can perform Stochastic Tractography and related analysis on DWMRI data. Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images.

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• SciCrunch
• 13 years ago - by Anonymous

3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City, Jan 2010.

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• SciCrunch
• 13 years ago - by Anonymous

Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site.

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• SciCrunch
• 13 years ago - by Anonymous

An algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web.

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• SciCrunch
• 13 years ago - by Anonymous

Software application that uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available.

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• SciCrunch
• 13 years ago - by Anonymous

The system is a web-based portal which allows vendors to review Federal Procurement Opportunities over 25,000. From the sites main navigation page, users can view opportunities and awards as well as view a variety of information and resources. FBO now contains Recovery and Reinvestment Act actions. Vendors / citizens may search, monitor, and retrieve opportunities. Government users may post, manage, and award opportunities when logged in using their password protected account.

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• SciCrunch
• 17 years ago - by Anonymous

A fast and robust software implementation of the popular Nonlocal Means for MRI-Rician denoising. It works by computing the non-local weights based on distances in a features space comprising the local mean value and gradients of the image. It can reach an acceleration factor of 20x over the original implementation, with an improved performance for medium-low SNR images. They use a bias correction step for Rician noise based on the well-known Conventional Approach. This software can be compiled either as a Slicer module or a stand-alone: http://www.nitrc.org/snapshots.php?group_id=518

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• SciCrunch
• 13 years ago - by Anonymous

Software framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation. The project is written in C++. It could be used both as a Slicer3 module and as a standalone commandline application.

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• SciCrunch
• 13 years ago - by Anonymous

Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection.

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• SciCrunch
• 12 years ago - by Anonymous

Segmentation tool that uses image analysis and machine learning techniques (Support Vector Machines). Image intensities from multiple MR acquisition protocols, after coregistration, are used to form a voxel-wise attribute vector which is used to perform the segmentation. Computer algorithms have started to complement expert-readings of MRI as they may improve throughput and consistency, in addition to providing more accurate quantitative measures of lesion type and volume. Computerized segmentation methods can also offer more precise measurements of longitudinal change of a lesion with disease progression or treatment response.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool for performing a per vertex statistical analysis across a population. The underlying statistical framework uses the R language.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.

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• SciCrunch
• 13 years ago - by Anonymous

A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply.

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• SciCrunch
• 13 years ago - by Anonymous

Provides series of modules which enable functions of Vascular Modeling Toolkit in 3D Slicer. Functionality includes vessel enhancement filtering, level set segmentation, centerline computation, network extraction and branch splitting.VMTK is available through the extension manager for 3D Slicer from version 4.6.2. Main difference to Slicer3 version is that now all VMTK modules come as one extension bundle. This should enhance the installation experience for users.

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• SciCrunch
• 13 years ago - by Anonymous

shapeAnalysisMANCOVA offers statistical shape analysis based on a parametric boundary description (SPHARM) as the point-based model computing method. The point-based models will be analyzed with the methods here proposed using multivariate analysis of covariance (MANCOVA). Here, the number of variates being tested is the dimensionality of our observations. Each point of these observations is a three dimensional displacement vector from the mean. The number of contrasts is the number of equations involved in the null-hypothesis. In order to encompass varying numbers of variates and contrasts, and to account for independent variables, a matrix computation is performed. This matrix represents the multidimensional aspects of the correlation significance and it can be transformed into a scalar measure by manipulation of its eigenvalues. Details of the methods can be found in its Insight Journal publication: http://hdl.handle.net/10380/3124

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• SciCrunch
• 13 years ago - by Anonymous

scikit-learn: machine learning in Python

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• SciCrunch
• 13 years ago - by Anonymous

Genetic maps for 94 inbred strains of mouse and imputed genotypes using the NIEHS / Perlegen resequencing resource. Combining with the 13,094 Wellcome Trust SNPs (Single-nucleotide polymorphisms), a set of 132,285 SNPs was compiled and is available for download. Using the mouse HapMap resource, it is possible to accurately impute the genotypes of the 94 strains at the 8 million SNPs discovered by the NIEHS/Perlegen mouse resequencing project. They imputed the genotypes at the NIEHS/Perlegen SNPs from the mouse HapMap SNPs and an additional set of 7,570 gap-filling SNPs provided by NIEHS/Perlegen. Since each NIEHS/Perlegen SNP probe has different quality, they classified roughly half of the SNPs as "high-quality" SNPs, which do not have missing genotype at any of the 15 resequenced strains. The imputed genotypes are available for the high-quality SNPs, which has estimated error rate of 0.27% for high-confidence imputed genotypes. In addition, the imputed genotypes for all 8 million SNPs are also available for download. Their estimated error rate is 0.37% for high-confidence imputed genotypes.

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• SciCrunch
• 17 years ago - by Anonymous

Public university in Barcelona, Spain that offers degree programs in social sciences, engineering, and arts and humanities.

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• SciCrunch
• 17 years ago - submitted by Eddy Kim